X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details Reservoir: 0.2 M sodium acetate, pH 7.0, 20% w/v PEG3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.98 α = 79.14
b = 67.49 β = 76.72
c = 67.63 γ = 88.89
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2014-09-19
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.68 50 98.5 0.058 -- 13.734 2.0 -- 29474 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.68 2.78 98.2 0.449 -- -- 2.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
-- 2.69 50.0 -- 0.0 -- 27981 1493 97.93 -- 0.1782 0.1749 0.2401 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.688 2.757 -- 116 1889 0.297 0.361 -- 90.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.918
Anisotropic B[1][1] 2.98
Anisotropic B[1][2] 2.15
Anisotropic B[1][3] 0.53
Anisotropic B[2][2] -1.45
Anisotropic B[2][3] -0.69
Anisotropic B[3][3] -1.23
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.014
r_gen_planes_refined 0.008
r_bond_other_d 0.002
r_dihedral_angle_1_deg 7.339
r_mcangle_it 7.093
r_mcbond_other 4.7
r_angle_other_deg 1.009
r_angle_refined_deg 1.76
r_mcbond_it 4.711
r_dihedral_angle_3_deg 18.221
r_dihedral_angle_4_deg 21.843
r_gen_planes_other 0.002
r_dihedral_angle_2_deg 34.72
r_chiral_restr 0.088
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5525
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 63

Software

Software
Software Name Purpose
SCALEPACK data scaling
REFMAC refinement version: 5.8.0103
PDB_EXTRACT data extraction version: 3.20